Field and atom-based 3D-QSAR models of chromone (1-benzopyran-4-one) derivatives as MAO inhibitors

Recent updates on structural insights of MAO-B inhibitors: a review on target-based approach

Parkinson's disease is a neurodegenerative disorder characterized by slow movement, tremors, and stiffness caused due to loss of dopaminergic neurons caused in the brain's substantia nigra. The concentration of dopamine is decreased in the brain. Parkinson's disease may be happened because of various genetic and environmental factors. Parkinson's disease is related to the irregular expression of the monoamine oxidase (MAO) enzyme, precisely type B, which causes the oxidative deamination of biogenic amines such as dopamine. MAO-B inhibitors, available currently in the market, carry various adverse effects such as dizziness, nausea, vomiting, lightheadedness, fainting, etc. So, there is an urgent need to develop new MAO-B inhibitors with minimum side effects. In this review, we have included recently studied compounds (2018 onwards). Agrawal et al. reported MAO-B inhibitors with IC50 0.0051 µM and showed good binding affinity. Enriquez et al. reported a compound with IC50 144 nM and bind with some critical amino acid residue Tyr60, Ile198, and Ile199. This article also describes the structure-activity relationship of the compounds and clinical trial studies of related derivatives. These compounds may be used as lead compounds to develop potent compounds as MAO-B inhibitors.

Multistage in silico approach to identify novel quinoline derivatives as potential c-kit kinase inhibitors

The type II-C-KIT signaling network has been extensively studied for its potential as a target for cancer treatment, leading to the investigation of quinoline derivatives as compounds with inhibitory effects on c-Kit kinase. In this study, a multistage approach was employed, including the creation of pharmacophore models, 3D QSAR analysis, virtual screening, docking investigations, and molecular dynamics stimulation. The pharmacophore evaluation included a data set of 29 ligands, which resulted in the generation of the ADDHR_1pharmacophore model as the most promising, with a survival score of 5.6812. The main objective was to utilize the atom-based 3D-QSAR approach for generating robust 3D-QSAR models aimed at identifying new TypeII-C-kit kinase inhibitors. The evaluations of these models have convincingly demonstrated their high predictive power (Q2 = 0.6547, R2 = 0.9947). Using atom-based 3D-QSAR data, a total of 7564 novel compounds were generated from R-group enumeration. Molecular docking and MM-GBSA study revealed that compound A1 exhibited the highest binding score of -9.30 kcal/mol and a Δ GBind value of -90.56 kcal/mol. The ZINC compounds were then screened using the pharmacophore model, followed by virtual screening, which identified ZINC65798256, ZINC09317958, ZINC73187176, and ZINC76176670 as potential candidates with promising docking scores. Among these, ZINC65798256 demonstrated the best binding interactions with amino acid residues, ASP810, LYS623, CYS673, and THR670 (PDB ID: 1T46). To further analyze the structural features and molecular interactions, molecular dynamics simulation was conducted for a time scale of 100 ns.Communicated by Ramaswamy H. Sarma.

Insilico design of an allosteric modulator targeting the protein-protein interaction site of 3 Phosphoinositide dependent Kinase-1: design, synthesis and biological activity

The signalling pathways in human cells mostly rely on protein-protein interactions (PPI) for their function. Such a PPI site in 3 Phosphoinositide dependent Kinase-1 (PDK1) is targeted to design the small molecule modulators. Based on the hotspot residues in its PPI site, a pharmacophore with seven different features was developed and screened against 2.9 million lead like compounds in Zinc database. A phthalazine derivative was identified as a potent allosteric inhibitor through virtual screening, molecular docking and 100 ns dynamics simulations. The modified hit possessed hydrogen bonds with Lys115, Arg131, Thr148, Glu150 as well as pi-pi stacking interactions with Phe157 which are the key residues in the PIF pocket of PDK1. Comparison between the free energy profiles by metadynamics simulation with the presence and absence of the modified ligand (MH) in the binding pocket indicates that the binding of MH enhances the hinge motion making PDK1 to adopt open conformation also and stabilizes the fluctuation of the end-to-end distance in αB helix of PDK1. The modified hit compound was synthesized, characterized and found to be cytotoxic to cancerous cells that are rich in PDK1 expression. These results propose that MH can serve as a new scaffold template for the design of novel drugs targeting PDK1 as well as promising allosteric regulator of PDK1 targeting its protein-protein interface.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-023-00160-6.